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- PDB-8ph1: Crystal structure of the metallo-beta-lactamase VIM1 with 3708 -

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Basic information

Entry
Database: PDB / ID: 8ph1
TitleCrystal structure of the metallo-beta-lactamase VIM1 with 3708
ComponentsBeta-lactamase VIM-1
KeywordsANTIMICROBIAL PROTEIN / Complex / metallo-beta-lactamase / inhibitor / zinc / indole carboxylate
Function / homology: / : / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / metal ion binding / : / Beta-lactamase VIM-1
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsCalvopina, K. / Brem, J. / Farley, A.J.M. / Allen, M.D. / Schofield, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust099141/Z/12/Z United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of the metallo-beta-lactamase VIM1 with 3708
Authors: Calvopina, K. / Brem, J. / Farley, A.J.M. / Allen, M.D. / Schofield, C.J.
History
DepositionJun 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase VIM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5944
Polymers28,0511
Non-polymers5423
Water5,567309
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-78 kcal/mol
Surface area9530 Å2
Unit cell
Length a, b, c (Å)39.470, 67.820, 40.180
Angle α, β, γ (deg.)90.000, 93.620, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Beta-lactamase VIM-1 / Class B carbapenemase VIM-1 / Metallo-beta-lactamase / Metallo-beta-lactamase VIM-1 / Metallobeta- ...Class B carbapenemase VIM-1 / Metallo-beta-lactamase / Metallo-beta-lactamase VIM-1 / Metallobeta-lactamase / Subclass B1 metallo-beta-lactamase VIM-1 / VIM-1 / VIM-1 metallo-beta-lactamase / VIM-1 protein


Mass: 28051.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaVIM, blaVIM-1, CAZ10_38240, CAZ10_38245 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q9XAY4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-YMF / 7-[(1~{S})-1-[(5~{R})-5-[(2~{R})-3-azanyl-2-methyl-propyl]-2-oxidanylidene-1,3-oxazolidin-3-yl]ethyl]-3-(1~{H}-pyrazol-4-yl)-1~{H}-indole-2-carboxylic acid


Mass: 411.454 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H25N5O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2.2M ammonium phosphate 0.1M TrisHCl, pH 8.5 / PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.81532 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81532 Å / Relative weight: 1
ReflectionResolution: 1.33→34.06 Å / Num. obs: 48336 / % possible obs: 99.7 % / Redundancy: 5.9 % / Biso Wilson estimate: 14.28 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.02 / Rrim(I) all: 0.051 / Net I/σ(I): 16
Reflection shellResolution: 1.33→1.36 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 3544 / CC1/2: 0.82 / R split: 0.747 / Rpim(I) all: 0.29 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→34.06 Å / SU ML: 0.1247 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 13.872
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1529 2494 5.16 %
Rwork0.1251 45824 -
obs0.1264 48318 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.75 Å2
Refinement stepCycle: LAST / Resolution: 1.33→34.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 32 309 2072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01152033
X-RAY DIFFRACTIONf_angle_d1.28092814
X-RAY DIFFRACTIONf_chiral_restr0.0898312
X-RAY DIFFRACTIONf_plane_restr0.0232383
X-RAY DIFFRACTIONf_dihedral_angle_d6.3647323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.360.23461420.18522505X-RAY DIFFRACTION99.18
1.36-1.380.18681520.15432521X-RAY DIFFRACTION99.26
1.38-1.410.18441180.14022517X-RAY DIFFRACTION99.4
1.41-1.450.19951540.13422515X-RAY DIFFRACTION99.26
1.45-1.480.191270.12972553X-RAY DIFFRACTION99.52
1.48-1.520.18071460.11632537X-RAY DIFFRACTION99.67
1.52-1.570.16481420.11152516X-RAY DIFFRACTION99.66
1.57-1.620.16911480.11872536X-RAY DIFFRACTION99.63
1.62-1.680.16681160.10432564X-RAY DIFFRACTION99.93
1.68-1.740.13651460.0982549X-RAY DIFFRACTION99.93
1.74-1.820.14981210.10572567X-RAY DIFFRACTION99.89
1.82-1.920.13691740.10332517X-RAY DIFFRACTION100
1.92-2.040.13311550.10422511X-RAY DIFFRACTION99.93
2.04-2.20.12571450.10662562X-RAY DIFFRACTION99.96
2.2-2.420.13231150.11032579X-RAY DIFFRACTION99.93
2.42-2.770.13421590.12232537X-RAY DIFFRACTION99.63
2.77-3.480.14911280.13822579X-RAY DIFFRACTION100
3.48-34.060.17751060.1472659X-RAY DIFFRACTION99.93

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